5 July 2023

 

There are some real bangers I’m having a look at this week, oh boy:

 

Evolution of a minimal cell. They took the Venter Institute’s minimal mycoplasma cell and tracked its evolution in vitro. Such a simple and cool idea, can’t believe it hadn’t been done before. Came out today, haven’t had a good look yet. https://www.nature.com/articles/s41586-023-06288-x

 

Evolutionary shortcuts via multi-nucleotide substitutions and their impact on natural selection analyses. tldr; if you assume that substitution mutations can only happen one SNP at a time, you highly underestimate positive selection, so here are better ways of analyzing genomes. https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msad150/7217158

 

Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities. Weirdo virus-ish transposon-ish DNA elements are a major mechanism of horizontal gene transfer in nematodes, and even more interesting, result in a selfish genetic element that gives rise to genetic incompatibilities. https://www.science.org/doi/10.1126/science.ade0705

 

Modelling genetic stability in engineered cell population. A mathematical framework for modeling the decay of synthetic gene circuits due to evolution. My personal favorite for the week, since I first started thinking about evolution from the point of view of synthetic biology. https://www.nature.com/articles/s41467-023-38850-6

Comments

Post a Comment

Popular posts from this blog

13 Aug 2023

There are lots of papers this week, buckle up Predicting evolutionary outcomes through the probability of accessing sequence variants . Thanks Sarah for sharing this one! This is such a simple but important idea. Essentially, evolution follows not only the contours of the fitness landscape but also the “genotype-accessibility landscape”, which is shaped by stuff like codon bias and biochemical mechanisms of mutation changing the likelihoods of some mutations. They look at some examples of this in fu. https://www.science.org/doi/full/10.1126/sciadv.ade2903   Purifying selection and adaptive evolution proximate to the zoonosis of SARS-CoV-1 and SARS-CoV-2 . These folks do some population genetics archaeology to try to put together what was happening with the genomes of SARS-CoV-1 and SARS-CoV-2 around the time they jumped into humans. They find most things are under purifying selection (which is generally the case with viruses as they “live on the (evolut...
Read more

23 July 2023

    Here are my picks of papers for the week:   Emergent coexistence in multispecies microbial communities . Álvaro Sánchez does some pretty neat, elegant work showing that if you break down a stable synthetic microbial community by studying all pairwise interactions of its members, almost every single time you’ll get one member of the pair outcompeting and excluding the other. The point of doing this is to show that ecological complexity isn’t a consequence of coexistence, but rather that coexistence is a consequence of ecological complexity. Not the first time I see this idea explored, but it’s a cool one. https://www.science.org/doi/10.1126/science.adg0727 , or open access here: https://europepmc.org/article/MED/37471535   Sequential mutations in exponentially growing populations. This theoretical paper seems to have some useful approaches to estimate the number of mutants in an exponentially growing population using branching processe...
Read more

3 Sep 2023

Back from travel and I had time to spot lots of interesting science to dump here, maybe too many this week. A lot of bacterial and phage microbial ecology this week, a dash of cancer, antibiotics, and covid. Lots of game theory! I like that the focus is changing week to week. We have:   Deep mutational scanning reveals the functional constraints and evolutionary potential of the influenza A virus PB1 protein Another week, another Lauring Lab paper. They assay 84% of all substitutions in the AH1N1 flu polymerase catalytic subunit, since it’s commonly involved in host adaptations when jumping species barriers. They compare their experimental data of the fitness effects of individual mutations to observational data from flu genomic surveillance. A lot of interesting lessons here, but I’ll note real mutational landscapes are a lot more constrained than the experimental data shows, in good part determined by mutation accessibility. https://doi.org/10.1101/2023.08.27.554986 ...
Read more